Wednesday, 29 July 2015

GCSE genes

As you will know, I am used to reporting on the long march of genetic science as it surges through the marshlands of blank-slate environmentalism. I expect we will be revising our understanding of human behaviour in the greatest change since the publication of Origins of Species. The telescope supplants naked-eye astronomy.

The story so far is that 58% of academic achievement can be explained by genetics. Now the same Plomin South London gang have taken a deeper look at individual school subjects, partialling out the common g factor of intelligence.

Pleiotropy is not the best word with which to start the title of a paper. Pleiotropy is the production by a single gene of two or more apparently unrelated effects. You knew that, but I just thought I’d tell you. Of course, I do not do headlines, but a typical British red top tabloid would scream: “GCSE genes found: for every one you get two exam passes free.”

Here is their abstract: Research has shown that genes play an important role in educational achievement. A key question is the extent to which the same genes affect different academic subjects before and after controlling for general intelligence. The present study investigated genetic and environmental influences on, and links between, the various subjects of the age-16 UK-wide standardized GCSE (General Certificate of Secondary Education) examination results for 12,632 twins. Using the twin method that compares identical and non-identical twins, we found that all GCSE subjects were substantially heritable, and that various academic subjects correlated substantially both phenotypically and genetically, even after controlling for intelligence. Further evidence for pleiotropy in academic achievement was found using a method based directly on DNA from unrelated individuals. We conclude that performance differences for all subjects are highly heritable at the end of compulsory education and that many of the same genes affect different subjects independent of intelligence.

In their introduction the authors say: Multivariate genetic analysis estimates the genetic contribution to the phenotypic correlation between traits and derives the genetic correlation, which corresponds to the correlation between genes that affect the two traits, independent of the heritabilities of the traits; the genetic correlation is an index of pleiotropy (the multiple effects of genes).

That sentence made me increase my coffee consumption. This is what I think it means: Correlations between traits are partly genetic, and multivariate genetic analysis estimates how much of those correlations are due to the same genes acting in common.

The authors used their very large twin sample to do the basic calculations, and also chose one twin at random to do the very different CGTA analysis of the influence of common SNPs on unrelated persons.

They start their results section by giving the old-fashioned statistics that I like, and then go on to the more complicated analyses of variance. Good stuff.

Here are the heritability estimates for intelligence and school subjects:

Note that the shared variance (effects due to family and schooling which children share) is minimal for intelligence, and small for specific school subjects.

When you control for intelligence (partial it out) then it would seem that Maths shows the biggest effect of schooling, the biggest of the small shared variance effects. English shows very small differential effects of schooling or family.

Summing up their results, the authors say: Our results demonstrate that educational achievement across a wide range of academic subjects from traditional core subjects of English, mathematics and science, to humanities, second language learning, business informatics and art at the end of compulsory education in the UK is highly heritable, with over half of the variance in children’s educational achievement explained by inherited differences in their DNA, rather than school, family and other environmental influences. These results are in line with our previous research at earlier school years and with results reported for core GCSE subjects. The slight difference in heritability estimates in core GCSE subjects results from including opposite sex twin pairs in the sample, which were not included in our previous study, resulting in more conservative heritability estimates. We have also demonstrated that this high heritability is not explained by intelligence alone, as the heritability remained high even after removing intelligence from the GCSE grades. This is consistent with our recent study that showed that high heritability of educational achievement is explained by many genetically influenced traits, not just intelligence.

In the most novel contribution of the present study, we showed that academic subjects at the end of compulsory education in the UK are to a large extent influenced by the same genes, even when intelligence is controlled. The genetic correlation between various academic achievement measures was substantial (.51–.88) and this includes traditional academic subjects of English, mathematics and science as well as art and language learning. The genetic overlap between GCSE scores and intelligence at age 16 was also substantial (.44–.69); however, genetic correlations were higher between GCSE scores than between GCSE scores and intelligence. Despite the genetic overlap between GCSE scores and intelligence, an intriguing finding is that pleiotropy among academic subjects is to a large extent independent of intelligence, as the genetic correlations were still substantial even after statistically removing intelligence from the GCSE scores (.49–.81).

It is possible that the strong genetic influence compared to the modest effects of shared family and school environments on academic achievement occurs because of the standardized curriculum in the UK. Environmental differences may be reduced in the UK because of its national standardized curriculum; heritability estimates could be high precisely because environmental differences are attenuated. In fact, it has been proposed that the heritability of educational achievement could be viewed as an index of equal educational opportunities. Empirical evidence provides some support for this hypothesis as the heritability of educational attainment has been reported to be higher and shared environmental influences lower in a centralized educational system as compared to a decentralized educational system, such as the United States.

This evidence for the highly pleiotropic nature of achievement in academic subjects and intelligence goes against the belief of specific learning abilities, such as mathematics ability versus ability in language.

This is a very good paper, making solid points. It points out that the calls for “a level playing field” are to be encouraged: they will boost overall ability, and increase heritability estimates. The authors also go through potential limitations of their study, and give possible answers and suggest possible research. Traditional papers have a lot to be said for them.

My O levels Maths teacher was excellent. Higher maths was another matter. It was taught by a bored physics teacher who made no concessions to the few students who went to his introductory lecture, secure in the knowledge that even fewer would sign up for the course. A pity.

Put otherwise: there is an intellectual level low enough that only a rather generalised intelligence is required to pass the exams in each subject. I bet there's also an intellectual level high enough that a rather specialised intelligence is necessary if the candidate is to shine.

Afterthought: what if GCSE also required one to play the piano, sing in tune, paint a decent portrait, toss off a sonnet, and bowl a decent leg-break?

i can't seem to find what their intelligence measure is - is it given along with the GCSE, such as a group administered paper-pencil measure? certainly the correlations might be even higher if that was a more reliable measure -- also, i imagine the bottom 2% of ability probably don't take the GCSE? i'm sure that was corrected for, but again the correlations would be higher if the very lowest of the low took both measures - makes me wonder how good the floor & ceiling of these measures is/are - i imagine the GCSE achievement measures have a good ceiling, but does their measure of intelligence also? oh for a good scatterplot! they've published much from this dataset before (e.g., www.pnas.org/content/111/42/15273.full) alas, i'm not very familiar with the GCSE - wish i'd have taken it!

The (full) web-based testing validation paper that refers to contains some detail and is here:

http://eprints.whiterose.ac.uk/3417/1/Haworth_2007_validation.pdf

GCSEs do have a good ceiling. They are typically taken when children are 16 but you'll find some teachers claiming the top 10% could polish them off aged 14. Especially in maths where it's common to pad that time out with a second GCSE in 'further' maths or similar.

merci beaucoup! overall looks like i should've been put out of business years ago by computerized testing - the stability from 10 to 12 years for the ability measure (r = .66, N = 987) doesn't look great, but overall the stats look plenty good enough - especially using branching/item sets so folks get enough items around their ability level - should put us 1:1 testers out of business, but things change so slowly i'm sure i'll make it to retirement unscathed:) thanks!